Compensatory nature of Chargaff’s second parity rule

Abstract

The second parity rule of Chargaff (A≈T and G≈C within one strand) holds all over the living world with minor exceptions. It is maintained with higher accuracy for long sequences. The question addressed in the article is how different sequence types, with different biases from the parity, contribute to the general effect. It appears that the sequence segments with biases of opposite sign are intermingled, so that with sufficient sequence lengths the parity is established. The parity rule seems to be a cumulative result of a number of independent processes in the genome evolution, with the parity as their intrinsic property. Symmetrical appearance of simple repeats and of Alu sequences in the human DNA strands, and other contributions to the Chargaff parity II rule are discussed.

Keywords:

• Chargaff’s second parity rule
• compositional bias
• characteristic sequence length
• gene direction
• compositional compensation

Acknowledgements

This work has been partially supported by a Fellowship of SoMoPro (South Moravian Program, Czech Republic) with financial contribution of the European Union within the 7th framework program (FP/2007–2013, grant agreement No. 229603), to Trifonov E.N. The authors are grateful to thoughtful comments of reviewers.